Our invention provides a practical way to extend the field of integrated optics to non-solid waveguide core materials. That is, we describe a way for guiding light on a chip through non-solid materials such as gases and liquids. Light can not only interact with these materials at the location of the active elements in the integrated device, the connections (“optical wires”) between elements can also occur through the non-solid materials. Before we explain certain background information relevant to our invention, it should be noted that, although we focus much attention to biomedical applications, the present invention is not limited to any specific application, biomedical or otherwise. The present invention may be applied to a broad range of problems, including but not limited to: the sensing of gases and liquids; single molecule spectroscopy (e.g., fluorescence); quantum optics and quantum information processing; optical measurements of extremely small volumes of gases and liquids; optical tweezers for manipulating tiny (microscopic) particles using light forces; implantable biomedical sensors, etc. Accordingly, except as they may be expressly so limited, the scope of protection of the claims at the end of this specification is by no means limited to the specific applications described herein.
Currently, there are a number of optical methods being used to improve human health and answer health-related scientific questions. These include both applications which are already well advanced (cell flow cytometry (Maltsev, V. P., “Scanning flow cytometry for individual particle analysis,” Rev. Sci. Inst. 71, 243 (2000); Ivnitski, D. et al., “Biosensors for detection of pathogenic bacteria,” Biosensors and Bioelectronics 14, 599 (1999)), blood measurements (Gifford, S. C. et al., “Parallel microchannel-based measurements of individual erythrocyte areas and volumes,” Biophysical Journal 84, 623 (2003)) as well as very fundamental questions regarding the human body (e.g., basic understanding and counting of single DNA molecules. Levene, M. J. et al., “Zero-mode waveguides for single-molecule analysis at high concentrations,” Science 299, 682 (2003)). Such single molecule studies are carried out to improve drug screening, mRNA expression profiling, and DNA sequencing. Castro, A., et al., “Single-Molecule detection of specific nucleic acid sequences in unamplified genomic DNA,” Anal. Chem., 69, 3915, (1997); Woolley, A. T. et al., “Direct haplotyping of kilobase-size DNA using carbon nanotube probes,” Nature Biotechnology 18 760 (2000)). At the same time, there is a continuing trend to increase the sensitivity of biomedical sensors and imaging methods, down to very small sample volumes (Webb, W. W., “Fluorescence correlation spectroscopy: inception, biophysical experimentations, and prospectus,” Applied Optics 24 3969 (2001); Lou, H. J. et al., “Femtoliter microarray wells for ultrasensitive DNA/mRNA detection,” Instrumentation Science and Technology 30 465 (2002)) and individual molecules (DNA). Another area where exquisite sensitivity is required is detection of toxic substances in the gas phase (e.g., in air). We will describe below some specific examples of state-of-the-art methodologies that are currently being used, and describe their performance and limitations. Then we will describe our novel approach with emphasis on how existing problems are addressed and solved.
(i) DNA Fluorescence with Single Molecule Resolution
There are a couple of methods for optical measurements on single molecules. A popular one is to observe them using diffraction-limited optics (Medina, M. et al., “Fluorescence correlation spectroscopy for the detection and study of single molecules in biology,” Bioessays 24, 758 (2002)). The principle of one technique—fluorescence correlation spectroscopy—is shown in FIG. 1(a). Problems associated with this method include the fact that only extremely small volumes on the order of fl are tolerable, and more importantly, that such setups are bulky in nature and cannot be scaled readily to multiple sample volumes.
A potentially significant improvement to some of these issues has recently been made by Levene et al. (Levene, M. J. et al., “Zero-mode waveguides for single-molecule analysis at high concentrations,” Science 299, 682 (2003)), who developed a detection method with single molecule sensitivity based on evanescent coupling of light from molecules trapped in sub-micron sized holes in metal films. The principle is shown in FIG. 1(b) where enzymatic synthesis of double-stranded DNA by DNA polymerase using fluorescently tagged nucleotide analog coumarin-dCTP was measured.
Using such zero-mode waveguides, the observation volume can be increased to the micromolar level. However, while this method is clearly ingenious, it can be seen from FIG. 1(b) that the setup is still rather cumbersome and involves optical paths for excitation and detection that are perpendicular to the sample plane. The metal film contains a large number of these zero-mode waveguides, which results in large parallelism. However, since the fluorescence is collected through a microscope objective, a large number of these holes are interrogated simultaneously and deliberate readout from a single hole is impossible. In addition, evanescent waveguide coupling is a concept that is currently pursued by many groups to couple optical signals into waveguides. However, it is highly inefficient as it relies on detection of exponentially decaying electric field values of the fluorescence signal. As a result, no transport of the optical signal through a waveguide or all-optical post-processing is possible.
(ii) Flow Cytometry of Small Volumes
Another area in which optical interactions with a liquid sample containing biological material are being studied is flow cytometry. This field is rather well developed and an advanced setup capable of individual particle analysis (Maltsev, V. P., “Scanning flow cytometry for individual particle analysis,” Rev. Sci. Inst. 71, 243 (2000)) is shown in FIG. 2(a).
In this case, a microchannel containing the specimen with a width of 10 μm is used. A laser is sent into this channel and fluorescence is detected perpendicular to the excitation direction. The important facts to note are that no waveguiding within the microcuvette is involved, measurements of multiple channels is impossible with this setup and the whole setup is composed of bulk optics.
Another example for a generic flow cytometry setup is shown in FIG. 2(b). In FIG. 2(b), a liquid sample containing potentially pathogenic bacteria is passed through a flow cell and the specimen is excited using a microscope objective in the perpendicular direction. This arrangement brings with it significant loss of the optical signal due to multiple interfaces between the sample space and the end of the microscope objective. In addition, only one channel can be excited this way as the focal depth of the excitation spot is very small and the excitation beam diverges quickly after it passes the flow cell. Leistiko et al. describe another realization of a microfluidic channel system for biological and biochemical applications Leistiko O, Jensen P. F. “Integrated bio/chemical microsystems employing optical detection: the clip-on.” [Conference Paper] IOP Publishing. Journal of Micromechanics & Microengineering, vol. 8, no. 2, June 1998, pp. 148-50. There, optical fibers are placed in etched grooves on a silicon substrate and covered with a pyrex slide. The light from the optical fibers is coupled into integrated waveguides in the silicon. However, they intersect an ordinary microcapillary which again leads to significant coupling losses into and out of the capillary leading to a coupling efficiency of only a few percent.
In light of the limitations and problems described above, and as discussed in greater detail below, we have invented a new approach to develop a planar integrated platform for such optical measurements with high sensitivity and the potential for massive parallelism. A presently preferred implementation of our invention is based on ARROW waveguides. (Miyagi, M. et al., “A proposal for low-loss leaky waveguide for submillimeter waves transmission,” IEEE Trans. On Microwave Theory and Tech. 28, 298 (1980); Duguay, M. A., et al., “Antiresonant reflecting optical waveguides in SiO2—Si multilayer structure,” Appl. Phys. Lett. 49, 13 (1986)). We will first describe the principle behind these waveguides and then explain several ways in which they may be used.
In conventional waveguides, light is guided in a medium with higher refractive index than its surroundings (e.g., silica fiber/air). When the refractive index situation is reversed (e.g., in microcapillaries) light cannot be guided in the central low-index region (core) and will leak out as shown in FIG. 3(a). A solution to this problem is to prevent the transverse components of the propagation vector from leaking out. This can be accomplished by adding Fabry-Perot reflectors in the transverse direction as is shown in FIG. 3(b). The high-index layers will reflect most of the light propagating in the transverse direction (vertical direction in FIGS. 3(a), (b)). The thickness t of the high-index cladding layer is chosen correctly to yield the desired interference.
It is important to note that these structures are well-known in optoelectronics and photonics where they have mainly been used as design tools for high-power and cascade lasers (Mawst, L. J. et al., “Design optimization of ARROW-type diode lasers,” IEEE Phot. Technol Lett. 4, 1204 (1992); Patterson, S. G. et al., “Continuous-wave room temperature operation of bipolar cascade laser,” Electronics Letters 35, 395 (1999)). In all applications, however, the ARROW waveguides were made using only solid-state semiconductor or dielectric materials. We are interested in ARROW waveguides where the low-index core is liquid or gaseous (Schmidt, H. et al., “Integrated optical spectroscopy of low-index gases and liquids using ARROW waveguides,” Integrated Photonics Research Conference, Washington, D.C. (2003)). It should also be pointed out that light guiding in low-index media is also possible using photonic bandgap structures (Joannopoulus, J. D. et al., “Photonic crystals,” Princeton University Press, 1995). However, such structures are extremely complicated to fabricate and cannot be used for some of the applications of interest here. They also rely on structures with long range periodicity which is not required for ARROW structures. In addition, fabrication of hollow core ARROW waveguides has been proposed using a different fabrication method (R. Bernini, S. Campopiano, and L. Zeni, “Silicon Micromachined Hollow Optical Waveguides for Sensing Applications”, IEEE J. Sel. Top. Quant. Elec. 8, 106-110 (2002)). Finally, a method for index-guiding through aqueous liquids in large diameter (several 100 microns) Teflon waveguides was demonstrated (Datta A, In-Yong Eom, Dhar A, Kuban P, Manor R, Ahmad I, Gangopadhyay S, Dallas T, Holtz M, Temkin H, Dasgupta PK. “Microfabrication and characterization of Teflon AF-coated liquid core waveguide channels in silicon.” [Journal Paper] IEEE Sensors Journal, vol.3, no.6, December 2003, pp. 788-95). Single-mode propagation and light confinement in gases is not possible with this approach.